Holy Cities do not affect missionary success odds at all? Are you 100% sure of that? It always "felt" that holy cities are harder to spread to, and I thought I read somewhere that it did supress the odds quite a bit, and have been playing most of my games under the assumption that Holy Cities are harder to infect. Hmmm...
Come to think of it, I've been under the impression there is a distance (from holy city) factor as well, though this is not based on anything and doesn't affect how I play to any appreciable degree.
I included the totality of the code that handles missionary spread in the previous post, and it's so simple that it's practically impossible to screw up the interpretation. Feel free to look yourself, if you won't take my word for it.
So yeah, I'm sure... FWIW I've never noticed that holy cities or distance would affect missionary spread at all either.
For those interested, I peeked at the corresponding Vanilla code as well, and it's functionally identical - except that in BtS you can modify the base spread chance in the XML (so one could, for example, effortlessly mod their Civ to have missionaries always succeed) whereas in Vanilla it's hard-coded.